Advanced Engines

Support for additional OPS modules

The basic engine setup is easy to do, and enables the core of OpenPathSampling’s functionality. However, some additional functionality can be added with very little effort, for engines where this might be relevant.

Velocity Randomization

There are two things an engine can do to support velocity randomization (i.e., RandomVelocities). First, an engine can implement a method called randomize_velocities that takes a snapshot and returns the new snapshot. If you do that, then we’ll just use that method.

Alternatively, you can implement apply_constraints. In this case, OPS will draw the random velocities, and then use your apply_constraints method to constrain velocities.

Shooting Point Velocity Modification

The original descriptions of TPS used two-way shooting with a “\(\Delta p\)” velocity modification. That is, the direction of the velocity on one particle was changed.

OPS has the ability to do this using the VelocityDirectionModifier, but this procedure becomes extremely complicated in condensed phase (periodic) systems with holonomic constraints. Therefore, OPS only allows this for engines where the snapshots have the n_degrees_of_freedom feature, which allows us to determine if there are any constraints. In addition, the engine can tell OPS not to bother removing linear momentum (e.g., if the engine represents a particle rolling on a surface, like our toy engine) by setting engine.ignore_linear_momentum = True.

MDTraj support

Several aspects of MDTraj support require an mdtraj.Topology object. The developer can add these by adding a property/attribute called mdtraj_topology to their engine. With this, you automatically get:

  • trajectory conversion to mdtraj.Trajectory, which enables output to various file formats, and integration with other projects such as nglview for trajectory visualization.

  • ??? TODO: can we make MDTraj CV support automated as well? Check for topol on first run? ???